config.yaml

# FOCA configuration
# Available in app context as attributes of `current_app.config.foca`
# Automatically validated via FOCA
# Cf. https://foca.readthedocs.io/en/latest/modules/foca.models.html

# Server configuration
# Cf. https://foca.readthedocs.io/en/latest/modules/foca.models.html#foca.models.config.ServerConfig
server:
  host: "0.0.0.0"
  port: 8080
  debug: True
  environment: development
  testing: False
  use_reloader: True

# Security configuration
# Cf. https://foca.readthedocs.io/en/latest/modules/foca.models.html#foca.models.config.SecurityConfig
security:
  auth:
    required: False
    add_key_to_claims: True
    algorithms:
      - RS256
    allow_expired: False
    audience: null
    validation_methods:
      - userinfo
      - public_key
    validation_checks: all

# Database configuration
# Cf. https://foca.readthedocs.io/en/latest/modules/foca.models.html#foca.models.config.DBConfig
db:
  host: mongodb
  port: 27017
  dbs:
    cwl-wes-db:
      collections:
        runs:
          indexes:
            - keys:
                run_id: 1
                task_id: 1
              options:
                "unique": True
                "sparse": True
        service_info: []

# API configuration
# Cf. https://foca.readthedocs.io/en/latest/modules/foca.models.html#foca.models.config.APIConfig
api:
  specs:
    - path:
        - api/20181010.be85140.workflow_execution_service.swagger.yaml
      add_security_fields:
        x-apikeyInfoFunc: app.validate_token
      add_operation_fields:
        x-swagger-router-controller: ga4gh.wes.server
      disable_auth: True
      connexion:
        strict_validation: True
        validate_responses: False
        options:
          swagger_ui: True
          serve_spec: True

# Logging configuration
# Cf. https://foca.readthedocs.io/en/latest/modules/foca.models.html#foca.models.config.LogConfig
log:
  version: 1
  disable_existing_loggers: False
  formatters:
    standard:
      class: logging.Formatter
      style: "{"
      format: "[{asctime}: {levelname:<8}] {message} [{name}]"
    long:
      class: logging.Formatter
      style: "{"
      format: "[{asctime}: {levelname:<8}] {message} [{name}]"
  handlers:
    console:
      class: logging.StreamHandler
      level: 20
      formatter: standard
      stream: ext://sys.stderr
  root:
    level: 10
    handlers: [console]

# Background job configuration
# Cf. https://foca.readthedocs.io/en/latest/modules/foca.models.html#foca.models.config.JobsConfig
jobs:
  host: rabbitmq
  port: 5672
  backend: "rpc://"
  include:
    - cwl_wes.tasks.run_workflow
    - cwl_wes.tasks.cancel_run

# Exception configuration
# Cf. https://foca.readthedocs.io/en/latest/modules/foca.models.html#foca.models.config.ExceptionConfig
exceptions:
  required_members: [["message"], ["code"]]
  status_member: ["code"]
  exceptions: cwl_wes.exceptions.exceptions

# Custom configuration
# Available in app context as attributes of `current_app.config.foca`
custom:
  storage:
    permanent_dir: "/data/output"
    tmp_dir: "/data/tmp"
    remote_storage_url: "ftp://ftp-private.ebi.ac.uk/upload/foivos"
  celery:
    timeout: 0.1
    message_maxsize: 16777216
  controller:
    default_page_size: 5
    timeout_cancel_run: 60
    timeout_run_workflow: null
    tes_server:
      url: "http://62.217.122.249:31567/"
      timeout: 5
      status_query_params: "FULL"
    drs_server:
      port: null # use this port for resolving DRS URIs; set to `null` to use default (443)
      base_path: null # use this base path for resolving DRS URIs; set to `null` to use default (`ga4gh/drs/v1`)
      use_http: False # use `http` for resolving DRS URIs; set to `False` to use default (`https`)
      file_types: # extensions of files to scan for DRS URI resolution
        - cwl
        - yaml
        - yml
    runs_id:
      length: 6
      charset: string.ascii_uppercase + string.digits
  service_info:
    contact_info: "https://github.com/elixir-cloud-aai/cwl-WES"
    auth_instructions_url: "https://github.com/elixir-cloud-aai/cwl-WES"
    supported_filesystem_protocols:
      - ftp
      - https
      - local
    supported_wes_versions:
      - 1.0.0
      - 1.0.1
    workflow_type_versions:
      CWL:
        workflow_type_version:
          - v1.0
          - v1.1
          - v1.2
    workflow_engine_versions:
      cwl-tes: 0.3.0, commit 7b44cb1
    default_workflow_engine_parameters: []
    tags:
      known_tes_endpoints: "https://csc-tesk-noauth.rahtiapp.fi/swagger-ui.html|https://tesk-na.cloud.e-infra.cz/swagger-ui.html"